M Hallett
January 2016
www.bci.mcgill.ca My lab website
www.bci.mcgill.ca/home/?page_id=811 Course Website
MTR 10:35am-11:25am
ENGTR – Trottier Building 2120
Jan 7th 2016 – April 15th 2016
\( {\tt michael.t.hallett@mcgill.ca} \)
Office: McIntyre 903
Office Hours: TBA
Mohamed Ghadie, Teaching Assistant
\( {\tt mohamed.ghadie@mail.mcgill.ca} \)
Office: TBA
Office Hours: TBA
| Exercise | Due Date | % of Grade |
|---|---|---|
| Assignment 0 | Monday, January 25, 2016 | 10% |
| Assignment 1 | Monday February 8, 2016 | 10% |
| Assignment 2 | Monday, February 22, 2016 | 10% |
| Midterm | Week of March 7-11, 2016 | 20% |
| Assignment 3 | Monday, March 21, 2016 | 10% |
| Assignment 4 | Monday, April 11, 2016 | 10% |
| Final Exam | TBA | 30% |
So Pubmed allowed researchers to identify papers that mentioned a gene (eg ESR). A lot of Principle Investigators (PIs) still primarily and only use PubMed to track their genes.
But what about results related to ESR that are derived from -omic/systems biology efforts.
Eg. every time an individual is sequenced, their ESR gene is sequenced and any mutations in this gene add to the global pool of polymorphisms.
Eg. every time a higher-order eukaroyte is sequenced, a homologue of ESR is sequenced (and may not be named ESR).
[But what about results related to ESR that are derived from -omic/systems biology efforts.]
Eg. every time a gene expression microarray is performed on a human sample, ESR levels are of course measured, since these microarrays cover the complete transcriptome. How can we get this information?
Eg. every time a mass spectrometry experiment is performed to identify proteins or protein interactions, ESR will have be measured too.
How can we explore this information? Is there an equivalent of PubMed?
[How can we explore this information? Is there an equivalent of PubMed?]
First off, how many such studies are there? 1 per year? 5 per year?
My daily NCBI automated search for the keyword “breast cancer” retrieves ~15 articles per day.
Can researchers afford to ignore this information and only look at the primary research?
In theory, GenBank '88, dbGap '07 and many other databases provide all of this information.
Bioinformatic software was necessary to perform complicated, statistical searches that allow researchers to track their genes in these datasets.
Managing biological information is a part of bioinformatics but not all
Bioinformatics is also the investigation of biological systems using tools from information science.
For example, my lab considers itself to be a breast cancer research lab whose primary assay is bioinformatics (as opposed to pull downs, PCR, microarray or other assays).
Often this is about hypothesis testing and biomarker discovery.
For example, the development of gene panels like Oncotype DX www.oncotypedx.com
For example, models of the genome, exome, transcriptome, proteome, protein interactome, methylomes, epigenome, … and many other -omic entities.
Hypothesis testing, biomarkers, and model building all require a tremendous amount of tools from biostatistics and computation.
The HapMap project that catalogs single nucleotide polymorphisms and other mutations in human populations.
Gene Expression Omnibus and other efforts seek to catalogue transcriptional (mRNA expression levels)
The Epigenome project that is attempting to catalogue all epigenetic modifications (e.g. methylation) in different types of human cells (e.g neuronal versus epithelial vs fibroblasts vs endothelial etc.).
Networks that capture which pairs of proteins interact within a cell or organism. Here this is a bacteria (Treponema palladium). Nodes are proteins and edges (lines) connect two proteins that have been determined to interact. Interactions can be between proteins within a complex (e.g. proteins that comprise the ribosome), proteins that phosphorylate other proteins within signalling cascasdes, protein chaperones that help other proteins fold, or …
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Historically,biological models are simple and deterministic
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The list goes on and on: